Tracking Git commits

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Core commits
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Recent Commits to bioperl-live:master

Minor doc fixes
Add ability to remove specific features, using primary_tag
add 5.20 (may remove 5.10 at some point)
add the two cyclic ref testers (not required for general users, but nice
fix test count, which fails if optional mem leak modules not installed
Add tests for memory leaks and weaken for Issue #81
Bio/Location/Split.pm: Final fix for issue #76. From now on,
t/data/dmel_2Lchunk.gb: Updated features locations to use current
Remove modules and tests (StandAloneBlast and WrapperBase) that now reside in bioperl-run
Removed empty file Bio/Tools/Run/hmmer3.pm, which seems
Bio/DB/Taxonomy/flatfile.pm: Fix for issue #80, changed DESTROY
Add travis-ci badge
Bio/Location/Split.pm: Removed the "$loc->is_remote" condition
FTLocationFactory.pm: Fixed a long-standing issue at "from_string()"
FTLocationFactory.pm: Adjusted from_string() subroutine to
hmmmer2 & hmmer3: Complete elimination of the use of '$_'
hmmer.t: Fixed minor mistake
hmmer3.pm: Fixed a bug where an homology line ending in CS or RF
genbank.pm: Fix for issue #70, removed the line at write_seq()
Bio/SeqFeature/Generic.pm: Fix for issue #76, adjusted "seq"
Run commits
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Recent Commits to bioperl-run:master

WBCommandExts.t: Fixed a pending TODO related to
Update Build.PL, MYMETA.json with build dependencies
no dependencies on any of the Test::* or Sub::Uplevel in any test (except maybe through Bio::Root::Test; in any case should not be frozen in the distro, but tests that break due to updates should instead be updated themselves.
Update Build.PL with config_requires and build_requires; add MANIFEST
Merge branch 'master' into topic/move_WrapperBase
fixed translate_params tests according to discussion at commit a6d0dc2; removed TODO around translate_params test
move StandAloneBlast* and WrapperBase* from root/Bio... to root/lib/Bio...
Merge branch 'master' of ../move_WrapperBase/bioperl-wb into topic/move_WrapperBase
test parameters independent of their order as issued on command line
Removed empty file Bio/Tools/Run/hmmer3.pm, which seems
Merge branch 'master' of https://github.com/bioperl/bioperl-live
giving new meaning to the term "git", moving Est2Genome.pm back where it belongs
adding back Est2Genome.pm -DOH
loosened validation for outfmt in BlastMethods to allow quoted multiple values (new blast+ feature); added tests for issue 12 to SABlastPlus.t
fix parsing edge case
issue 12: changes to _translate_params that allow quoted option values
POD updates
Really die if EMBOSS is not found
Merge branch 'master' of github.com:bioperl/bioperl-live
Merge pull request #71 from nathanweeks/issue/bio-seqfeature-lite-strand
Ext commits
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Recent Commits to bioperl-ext:master

moved Bio::Tools::HMM and Bio::Ext::HMM into their own distro, got them compiling cleanly. tests not passing yet
use UPPPER_TOL to catch the case when the expectation maximization step
fixed Vitebi typo
Fixed the typemap and also a memory bug in viterbi function in HMM.xs
adding FEEDBACK:Support section to pod
Bump to 1.007 (similar to trunk)
ext patches (courtesy Thomas Jahns)
get rid of some unended comment warnings from C compiler
-fPIC needed for lib construction
include errno definition
removed DEBUG=1
IUPAC DNA support
IUPAC DNA test case
Add some helper code and tests to demo evalue oddities (bug 1857); casting issue?
Add cast to correct pointer type (get rid of warnings)
update version to last bioperl release
bug 2329
bug 2074/2329
Removed Aaron's old test script (now in t/staden_read.t). Do we modify master ext makefile to account for this?
bug 2074
Bioperl-DB (BioSQL)
RSS

Recent Commits to bioperl-db:master

Minor POD edits and reformatting
Add some useful example code
updates since last release
update skipped files
add MANIFEST.SKIP
buzgilla -> redmine
[RT 44466] remove corba-related scripts, now obsolete
squash perl 5.12 warning
ignore conf file
add minimal .gitignore file
weird duplication removed
committing patch for bug #2958
test commit to check SVN::Notify
Build.PL now checks for DBD drivers and attempts to DTRT
remove MANIFEST.SKIP
update Changes
fix empty POD section
some pod cleaning
main trunk version is wrong
* 02species.t now compared to similarly behaving instance, also creates comparable array
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